DNA tennplates for transcription are continuously damaged by extrinsic factors such as radiation and chemical agents, as well as by products of endogenous metabolic processes. Maintenance of DNA integrity and high fidelity in transcription are crucial for life processes. DNA damage impairs transcription and triggers a variety of cellular responses, including DNA repair pathways, signaling pathways that activate cell cycle checkpoints, apoptosis, transcription, and chromatin remodeling. Defects in DNA repair or the processing of DNA damage can lead to cancer or other human diseases. It is inevitable for RNA polymerases to encounter DNA damage during transcription. Certain types of DNA lesions allow RNA polymerase bypass, while others completely block transcription. RNA polymerase 11 (pol II) bypass frequently results in mutagenesis at RNA, generating mutant proteins. In contrast, arrest of pol II by DNA lesions signals a specific DNA repair pathway to correct the damage and maintain the integrity ofthe DNA. The goal of my research is to understand the mechanisms of these cellular DNA damage processing pathways through an integrated multidisciplinary combination of chemical, structural, biochemical, and molecular biological methods.